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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1878 by gezelter, Mon Sep 10 18:38:44 2012 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 233 | Line 233 | namespace OpenMD {
233  
234        kinetic *= 0.5;
235        eTemp =  (2.0 * kinetic) /
236 <        (info_->getNFluctuatingCharges() * PhysicalConstants::kb );
236 >        (info_->getNFluctuatingCharges() * PhysicalConstants::kb );            
237      
238        snap->setElectronicTemperature(eTemp);
239      }
# Line 324 | Line 324 | namespace OpenMD {
324        Molecule* mol;
325        Atom* atom;
326        RealType charge;
327 –      RealType moment(0.0);
327        Vector3d ri(0.0);
328        Vector3d dipoleVector(0.0);
329        Vector3d nPos(0.0);
# Line 372 | Line 371 | namespace OpenMD {
371              pCount++;
372            }
373            
374 <          MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
375 <          if (ma.isDipole() ) {
377 <            Vector3d u_i = atom->getElectroFrame().getColumn(2);
378 <            moment = ma.getDipoleMoment();
379 <            moment *= debyeToCm;
380 <            dipoleVector += u_i * moment;
374 >          if (atom->isDipole()) {
375 >            dipoleVector += atom->getDipole() * debyeToCm;
376            }
377          }
378        }
# Line 624 | Line 619 | namespace OpenMD {
619    }        
620    
621    /**
622 <   * Return intertia tensor for entire system and angular momentum
623 <   * Vector.
622 >   * \brief Return inertia tensor for entire system and angular momentum
623 >   *  Vector.
624     *
625     *
626     *
# Line 705 | Line 700 | namespace OpenMD {
700      
701      return;
702    }
703 +
704 +
705 +  Mat3x3d Thermo::getBoundingBox(){
706 +    
707 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
708 +    
709 +    if (!(snap->hasBoundingBox)) {
710 +      
711 +      SimInfo::MoleculeIterator i;
712 +      Molecule::RigidBodyIterator ri;
713 +      Molecule::AtomIterator ai;
714 +      Molecule* mol;
715 +      RigidBody* rb;
716 +      Atom* atom;
717 +      Vector3d pos, bMax, bMin;
718 +      int index = 0;
719 +      
720 +      for (mol = info_->beginMolecule(i); mol != NULL;
721 +           mol = info_->nextMolecule(i)) {
722 +        
723 +        //change the positions of atoms which belong to the rigidbodies
724 +        for (rb = mol->beginRigidBody(ri); rb != NULL;
725 +             rb = mol->nextRigidBody(ri)) {          
726 +          rb->updateAtoms();
727 +        }
728 +        
729 +        for(atom = mol->beginAtom(ai); atom != NULL;
730 +            atom = mol->nextAtom(ai)) {
731 +          
732 +          pos = atom->getPos();
733  
734 +          if (index == 0) {
735 +            bMax = pos;
736 +            bMin = pos;
737 +          } else {
738 +            for (int i = 0; i < 3; i++) {
739 +              bMax[i] = max(bMax[i], pos[i]);
740 +              bMin[i] = min(bMin[i], pos[i]);
741 +            }
742 +          }
743 +          index++;
744 +        }
745 +      }
746 +      
747 + #ifdef IS_MPI
748 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMax[0], 3, MPI::REALTYPE,
749 +                                MPI::MAX);
750 +
751 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMin[0], 3, MPI::REALTYPE,
752 +                                MPI::MIN);
753 + #endif
754 +      Mat3x3d bBox = Mat3x3d(0.0);
755 +      for (int i = 0; i < 3; i++) {          
756 +        bBox(i,i) = bMax[i] - bMin[i];
757 +      }
758 +      snap->setBoundingBox(bBox);
759 +    }
760 +    
761 +    return snap->getBoundingBox();    
762 +  }
763 +  
764 +  
765    // Returns the angular momentum of the system
766    Vector3d Thermo::getAngularMomentum(){
767      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
# Line 864 | Line 920 | namespace OpenMD {
920    }
921  
922    RealType Thermo::getHullVolume(){
867 –    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
868 –
923   #ifdef HAVE_QHULL    
924 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
925      if (!snap->hasHullVolume) {
926        Hull* surfaceMesh_;
927 <
927 >      
928        Globals* simParams = info_->getSimParams();
929        const std::string ht = simParams->getHULL_Method();
930        
# Line 901 | Line 956 | namespace OpenMD {
956        // Compute surface Mesh
957        surfaceMesh_->computeHull(localSites_);
958        snap->setHullVolume(surfaceMesh_->getVolume());
959 +      
960 +      delete surfaceMesh_;
961      }
962 +    
963      return snap->getHullVolume();
964   #else
965      return 0.0;
966   #endif
967    }
968 +
969 +
970   }

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